Joao Magalhaes from the Human Aging Genomic Resources group has announced the development of a new web portal entitled Digital Ageing Atlas to integrate molecular, physiological and pathological age-related data:

http://human.ageing-map.org/

The goal is for this portal to serve as the first centralized collection of ageing changes and pathologies. It allows users to search and retrieve age-related changes at different levels, allowing a better understanding of the interplay between such changes and obtain new insights. They also think this will be an important new resource for modelling and for the systems biology of ageing and hope you will find it useful. Although so far they focused mostly on human ageing, a preliminary mouse version of the portal is online already.

All comments and suggestions are very much appreciated. The aim is for this resource to be developed and expanded in collaboration with the research community so anyone wishing to collaborate with them on this project is welcomed.

contact:
Joao Magalhaes, PhD
Human Ageing Genomic Resources

http://genomics.senescence.info

In a recent article in Cell Metabolism, Piper, Partridge, Raubenheimer and Simpson report that Dietary restriction (DR) and mutations in nutrient signaling pathways can extend healthy life span in diverse organisms.  Studying the interaction between these interventions should reveal mechanisms of aging, but has yielded some apparently contradictory results.  A multidimensional representation of nutrition, called the geometric framework, can better describe the responses of life span and other traits, including metabolism, and can reconcile these apparent contradictions.  They compare the response of Life Span to Nutrient Balance in Different Genotypes using insects like the fruitfly Drosophila melanogaster, the queensland fruitfly, Bactrocera tryoni and the field cricket Teleogryllus commodus. They provide examples showing that it is more informative to analyze DR in terms of dietary balance and that dietary optimization for life span is critical for studies examining the biology of again and other traits.

This preliminary assembly represents >20x coverage of the genome.    Because of the lack of annotation, one needs to use BLAST to find naked mole-rat contigs from your gene(s) of interest (he recommends using guinea pig genes as query).  They are working to add some basic annotation so users can at least quickly search for homologs of genes of interest.

contact Joao Magalhaes  aging@liverpool.ac.uk

Arctic tern. Image compliments of EOL.org

According to the BBC an Arctic tern (Sterna paradisaea) at least 30 years, 2 months and 23 days old was recaptured on Farne Islands this summer. Although this is the oldest Arctic tern recorded in the United Kingdom, the longest lived Arctic tern as recorded in AnAge, the animal longevity database, is 34 years old.

Commensal relationships between insects and their microbiota have been little studied and are not well understood.  However, recent studies have suggested that there are more of these relationships than previously thought.

Schistocerca gregaria, the desert locust

Schistocerca gregaria, the desert locust, is known to exploit the production of common metabolites by its indigenous gut flora (Charnley et al., 2000). One such chemical, guaiacol, is used as a key component in a pheromone which promotes the aggregating behaviour of this locust species. Some of the organisms found in the desert locust hind gut are Escherichia coli, Enterobacter liquefasciens, Klebsiella pneumoniae, Enterobacter cloacae, Pantoea agglomerans and various Gram positive cocci.

A more recent study by Charnley et al. (2010), investigates the effect of both starvation and insect age on the diversity of the gut microbiome of adult S. gregaria. Analysis of bacterial 16S rRNA sequences allowed the identification of species that are not culturable by incubation. However, only one novel uncultured member of the Gammaproteobacteria was identified, present in the commensal flora of locusts within all focus groups (fed, starved, young and old).

The results of this work suggested that diversity of the gut microflora in desert locusts increases with insect age and starvation. Whilst starved insects are more prone to disease, likely because they compromise on immune defense, an increase in the diversity of Gammaproteobacteria in the starved locust population may actually provide an improved defence due to their role in colonization resistance, whereby the presence of one species prevents colonization by another through competition.

This study indicates that the changes in the diversity profile of the gut microbiota in locusts may benefit the host in terms of colonization resistance against pathogens. Another recent study published in Nature earlier this year (Wang et al., 2010) explores the human gut microbial gene catalogue, or ‘metagenome’, describes the diversity of the human gut flora in terms of minimal gut bacterial genome and identifies a common ‘core’ of bacteria in healthy individuals. Overall, the study by Wang et al. found that a decrease in bacterial diversity in the human gut was associated with obesity and common bowel diseases.

Key Reference
Dillon RJ, Webster G, Weightman AJ, Charnley AK (2010) Diversity of gut microbiota increases with aging and starvation in the desert locust, Antonie van Leeuwenhoek, Vol. 97, pp. 69–77 DOI:10.1007/s10482-009-9389-5

Guest post by intern Catriona Smith

NPR just posted a graphical timeline showing the longest lived organisms on Earth and when they were born in history. Lifespans range from King’s lomatia at 43,000 years to Galapagos tortoises at 150 years.

We have just released LigerCat v. 2.1 – with new features and faster search. LigerCat it is a tool that allows you to search PubMed using words or even a DNA/protein sequence. The articles retrieved are processed to create a tag cloud showing an overview of important concepts and trends. The Medical Subject Headings or MeSH descriptors are combined and weighted by frequency (more frequent terms have a larger font size) to create the cloud. Clicking on one or more MeSH descriptors in the tag cloud adds it to the box on the right of the cloud and LigerCat searched PubMed for those terms instantly. Selecting more than one term finds articles tagged with all selected MeSH descriptors.

MeSH Cloud and Publication History for Alzheimer Disease

New features

• Publication History graphs – In the Articles Search a Publication History graph is displayed in addition to the MeSH tag cloud. This is an interactive graph. Mousing over the graph will highlight years and display the number of articles from that year that your search retrieved. Clicking on the bar for that year performs the search in PubMed and takes to that result page. In the Genes Search, the graph will not take you to PubMed but you still can see how many articles related to the query sequence were published in each year.
• Code snippet available so you can put a MeSH cloud on your blog or home page

Just click on the Share tab to get a code snippet for the cloud.

The embedded Alzheimers Disease cloud looks like this:

Steve Austad’s paper in Journal of Comparative Pathology (PubMed), Methusaleh’s Zoo: How Nature provides us with Clues for Extending Human Health Span, promotes the idea that “exceptionally long-lived organisms have important roles to play in our future understanding of the causal mechanisms and modulation of ageing.” Austad writes that most of what is known about the aging process is derived from experiments performed on short-lived laboratory species like Drosophila melanogaster, Caenorhabditis elegans and Mus musculus. He suggests that studying long-lived species such as naked mole-rats (Heterocephalus glaber) and some bats like Myotis brandti that lives for 41 years, might offer insight into the mechanisms of the aging processes. There are many more species to discover and study. As Austad concludes: “However, with the dramatic acceleration in our genome sequencing capability, it is likely that new investigatory tools for these species of exceptional gerontological interest will be developed at an accelerating pace. The role of Methusaleh’s Zoo in ageing research is likely to blossom in the near future.”

Scientists from Université de Rennes use an usual organism for their research, the sub-Antarctic wingless fly, Anatalanta aptera. This fly is interesting because it has a long imaginal life thus offering a good model to study evolution and senescence. A study recently published in Biology Letters showed that contrary to expectation older flies recovered better after experiencing cold temperatures. According to the authors, “our results both challenge the generality of the prediction that ageing impairs rather than improves performance in thermal biology and highlight the scarcity of studies on the subject.”

The new gene discovered in mouse (Mus musculus), Rps23r1, decrease levels of toxic proteins that are linked to the formation plaques and tangles in the brains of Alzheimers disease patients. Published today in Neuron and the result of a worldwide collaboration of seven institutions, the research identifies the new gene and demonstrates how it reduces the levels of protein phosphorylation of key proteins involved in Alzheimers disease pathology. “Our studies reveal a new target/pathway for regulating AD pathologies and uncover a retrogene and its role in regulating protein kinase pathways,” write the authors in the articles abstract. Read more at Eureka Alert, Burnham Institute for Medical Research, Science Daily.